Plant Circular RNA Database

Detail information of Os04g0271000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0271000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_023249
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11317806-11321776  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							Os04g0271000						
					
						Parent gene annotation
						
							NAD+-dependent histone deacetylase, Seed development (Os04t02710
00-01);Similar to SIR2-like protein. (Os04t0271000-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0271000_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						seed
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os04t0271000-02:6
Os04t0271000-01:6

General Information
CircRNA Name	Os04g0271000_circ_g.1
ID in PlantcircBase	osa_circ_023249
Alias	NA
Organism	Oryza sativa
Position	chr4: 11317806-11321776 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	Os04g0271000
Parent gene annotation	NAD+-dependent histone deacetylase, Seed development (Os04t02710 00-01);Similar to SIR2-like protein. (Os04t0271000-02)
Parent gene strand	-
Alternative splicing	Os04g0271000_circ_g.2
Support reads	1
Tissues	seed
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os04t0271000-02:6 Os04t0271000-01:6

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TTGTTATTTAGTTGCACGTACCTGAAGATTTACAATAGCCACCCTCCCCCCATTCTTCAGTGAC
AACAGAGGCATATTACAAGCAGGAGTAATCTGCAGAcagaaaatcaacaggccattcaatggaa
gagctcgaacagccgcaaccatcactaaagttgaatgtcaatagcatgacaaacggtctattca
ttgatgtt

									
								

					

						Assembled circRNA sequence  
						
							NA
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							NA						
					

						Genomic sequence
						
							CAGAAAATCAACAGGCCATTCAATGGAAGAGCTCGAACAGCCGCAACCATCACTAAAGTTGAAT
GTCAATAGCATGACAAACGGTCTATTCATTGATGTTTCTCTACAAAAGTAACAAGTGTCCTGTT
GTGAAATATGCCACAGACCTCAAATGTCTACTCGGGAACTTTGAATGCTCCAACATACCTCTGC
AAAGAAAATGGTTGCTCCTTTAGTACTACAGGCTTCATGTCAGGTCTTTCAGGAAAGGAAACCT
GTTGGTAAGTCAGAATAGTTTAATCATATATCACTATATCCATATAATATAATGGAGAAATATT
TTACACATATATATTTGGTAATTTGAGAATTAGCTTCTAACATCCATGCTATTTCAGAAGAAAA
TGACTGGTTTTGTTAGTATCAGCTACTAAAATATACTTCTACCATCACTAGATACATGTCATTC
TTGCTATTTTCTTCCCAAATATGTCAGTCTAGAAATTTCAAGATGGCTGTTCAATCTACTTTTA
GTGACTAGTTTCTATTTCGAAGATAATTTATGCCTCTAACCTAGAGTAATGCACAATTCTAAGA
GTGGATCTGGCTTTGCCGGTGGTTGGGGACGTCAGCGACGACGATGTAGGTCAGCTCTTTTCAT
TCCTACCCCTTCCCCTACTACCGCCTGCTTCTCCAGGACCGGTTTATCCCCTTGATTTTGCCTT
TGTCCTCTAGTTTTTCCCGCAAGGCGGAGGCAACGTGAGGCGGAGCGGACGCCTTACACCCTGG
CAGTGCCTTGCCGCCTTAGGAACACTAAGGCGAACGCCTTAACAACCATGAAACTACAACTTAC
AGCAAAATAGACTAATGTGAGAGTTCATTCTCCGAAAGTTGTTTGTCTACTAAGTTTGCAATAT
TAGAATGAAATTTGAAACTTGAATTTGTGTTACCTTGCTGAGTTGTGTTGATTGTTCATTTGAA
CACCTTGTTGGCTTGTTATAAATTAGCATAATACATGTCCATTTTTATCTTTTCCTTGTGTTGT
AAACTTGCGTACACTATTTTACTATGTTGAGGTAAGGTAAGTCATGAGTATATTCATGAATAAC
TCAAAATCTAATCTAGAGTTTTTCTTTTTAACTCCACCACTGGAATATAGTACCCTCTACCCGC
TAGCCTCTATATCAACCCCAATCTGCTATGACCCTGCTATATGCTATTTAGAACTTTGCTTGCC
ATTGCTAAACAAATGCTCTCAGTCATAAACAAATGATCTTTCTTCTCCAACATGGTATAAATGA
ATGGCCAAAATTTCATTTAATCTACCCTTTTTATCCTTATGAATAAGTCTACAATGAGAACGGA
GTAGCTATCCATAATCTATTTGTTCTCGATTGATCAAAGAGTATGTTGATGTACTATCAGTTAA
ATAATTGCACAACCTCAACTGATCGAAGAAATGGCAAAGGTGCTCGCAAGCCATGAATGCTTGT
TACTCGGAGAGTCCATCTCACGCATTTTTCTGCAAAACAAAAGCAGTGGTGCGGTTTGAGTTAA
TAAGCAATTCAAATCTATCTTCTAGGATAAAACAGGCTAAAATATCATTTTGTCCATCGAGTTG
TTGAGATGATACCGAGAATTGCTAAGGAAGATCCTATGAAAAAATACTATTATTTATGGATGGA
CACAACATAAAATAACCGTGTATCACATTTGGTAGTATGCCTATGATATTGAGACTATAGTTCG
AAATAACCTGATAATTCTTGTTGTTCAACATCTAACTAATGATACAGCTTTAATGATAACAGTA
TTCAGCTTTATTAACTAACCTCAGTTTGTTGTACGTAACTAAAAGCAATGTTCAAAACTAGATA
AGAATGACAATGCGAGAGATGGTGAGATGATCGTACTTTTGACCGAGTTCCGGAGACTAATTTG
AACAAAGTCAGTACGAATATATGGAGGGATACGCAGATTCATCATATACATAACCCCAGCAATG
ACCTGCACTAACACGGTTAAATAGCTACCGCAAGGGGATGAAATAGAAACAAATGAAACTCACT
AACATACCTACCTTATCCACAAGTCCATGAATGACAAGGCTTGCCTTTTTATCCTTCGGAGTTG
CCTGAATACGAAGGAGACAAGAAATGAAAAAAAAATATCTGTCTGCATCTCTTTTGGGGATTTA
TCACATGTCATTGTAAACTTTCAATATTTATCTACATTACAAATATACATATATCCATATATGA
CAATGTAATCTATGTTTATTAATTATTATATTACAATCTTGACCATTAAAAGGCTCATTTTTTT
AAGATGAGCAAAATGACCAATGTTGTATTTTGAAAATTCTGGAAGTATAACCACTTAGTAGATT
TCACATTTTAAAAACTACTCCCTCCAATCCTTAATAGATGATGTATTAGAATTTTGCTCATCAG
CCAAGACACCTGTGTAAAAGACCAAATTGTCTTCATTGTTATGAGCATCATAGGGTTAGGGTCT
GAAGACCGAGATTAGAATTAGGGCTCTGGCCCTTGGTCAACCATTCAGCCAGCCAGGAGCTCTT
CCAAACCACTAGTCACCAGCTAAAGGCACTAGACTGTATTGGAGAATAGAGGAAAACTAGAATC
CATCATTCCTTGTTACCCAAAAGTGTGTCACAATAACCTTCTGTCCTAGGCATCTCCAAATCAA
AGAAGAATGGTAACAACTTGTGCAAGTGCAACTAATAACTAACCAAAATATATAATAAAGCAAT
AACTGGTCTCTAAATTCTAACTTACTCGCCCTCTCTCCTGCCTTTAACTGGCATAACACCTCTG
CTGGTTACTGTGTGATAACTCCTACTGCACCATGTCTCATATAGCTCCGTCTAATATGGCTCCA
TGCAGCCATGGCAAAACATCATTTAATTCATTCATTAGCTGTCACGGGCATTAGGTCATGAGGC
CAAGGCCCATGGATAGCCCATACCAGTTAAGTTAGAGATAAGATAAGATTGAATCTTACTTAGG
GGTCAAGTTGTACCATCTATAAAAGGATGGGATTATGTCTATTATCAATTAAGCAATGAATATC
AATTAGTCTAATATCTCCCTTCCCGTAATGTTCTTCTCCCTAGCCTAAATCTACATCCCTTCTC
CACGAGCCGACGCCACCCAGTTATCCTCCCGGCGGTGGTTATCTCGCCATGGCCTTGGGTTGTG
ACATTAGCTCAGTCATATGCCTATTTGAAATGAACAGTTGGCTGCACATTCAAAACTAGCACAT
GAATGAACCCATGAGCATGTGTAATCGAATATTTGAGAAATATGGATGGAAAGCATGTATTTAT
GGTTCTTTGGATTGTACATAACCTGATTAAGTCTATACTAGTAAATGCCCTTTGGATGGTTATG
CTTGGGAAGGTAAAATTCAAATAACATTGCATTATGAAGGAAGGGGTATATAGGACAGACAAGT
AAAAAGTTGTCTTGAGGTGATAGTATGATTTATATCTGGGAACAAAATATTAACCTAGAATGCA
AATATTCAAAAATGGAGAGAGCAAAAGTTGCATCAATTGTACACCATGTGCATGTAAATACCAT
ATTTGCAATTTCTAACTTTATAATGGATCAGGAATCCAATTATAAACCCCAAGTCTAAGTATAC
AAGTTGAAGCAGTACAAACTACAAATTTTGTCAGAAGCATAAAGAAACAGCCATATAACAAACT
TGAAATTTCCAAAACATGCCAAAAGATATTTTAATAATTTATATGTAGCCATAAATACTAACAT
CCATGAGTTGAGTCATAGTTTAGTGCTACATAGAAAGACCTTACGAAGGAAGAACCATAACGTG
CATTCAATTTAGTGCTTCTCAAGACTTAATATTGTTATTTAGTTGCACGTACCTGAAGATTTAC
AATAGCCACCCTCCCCCCATTCTTCAGTGACAACAGAGGCATATTACAAGCAGGAGTAATCTGC
AGA
						
					

			
		

Sequences
Splice junction sequence	TTGTTATTTAGTTGCACGTACCTGAAGATTTACAATAGCCACCCTCCCCCCATTCTTCAGTGAC AACAGAGGCATATTACAAGCAGGAGTAATCTGCAGAcagaaaatcaacaggccattcaatggaa gagctcgaacagccgcaaccatcactaaagttgaatgtcaatagcatgacaaacggtctattca ttgatgtt
Assembled circRNA sequence	NA The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	NA
Genomic sequence	CAGAAAATCAACAGGCCATTCAATGGAAGAGCTCGAACAGCCGCAACCATCACTAAAGTTGAAT GTCAATAGCATGACAAACGGTCTATTCATTGATGTTTCTCTACAAAAGTAACAAGTGTCCTGTT GTGAAATATGCCACAGACCTCAAATGTCTACTCGGGAACTTTGAATGCTCCAACATACCTCTGC AAAGAAAATGGTTGCTCCTTTAGTACTACAGGCTTCATGTCAGGTCTTTCAGGAAAGGAAACCT GTTGGTAAGTCAGAATAGTTTAATCATATATCACTATATCCATATAATATAATGGAGAAATATT TTACACATATATATTTGGTAATTTGAGAATTAGCTTCTAACATCCATGCTATTTCAGAAGAAAA TGACTGGTTTTGTTAGTATCAGCTACTAAAATATACTTCTACCATCACTAGATACATGTCATTC TTGCTATTTTCTTCCCAAATATGTCAGTCTAGAAATTTCAAGATGGCTGTTCAATCTACTTTTA GTGACTAGTTTCTATTTCGAAGATAATTTATGCCTCTAACCTAGAGTAATGCACAATTCTAAGA GTGGATCTGGCTTTGCCGGTGGTTGGGGACGTCAGCGACGACGATGTAGGTCAGCTCTTTTCAT TCCTACCCCTTCCCCTACTACCGCCTGCTTCTCCAGGACCGGTTTATCCCCTTGATTTTGCCTT TGTCCTCTAGTTTTTCCCGCAAGGCGGAGGCAACGTGAGGCGGAGCGGACGCCTTACACCCTGG CAGTGCCTTGCCGCCTTAGGAACACTAAGGCGAACGCCTTAACAACCATGAAACTACAACTTAC AGCAAAATAGACTAATGTGAGAGTTCATTCTCCGAAAGTTGTTTGTCTACTAAGTTTGCAATAT TAGAATGAAATTTGAAACTTGAATTTGTGTTACCTTGCTGAGTTGTGTTGATTGTTCATTTGAA CACCTTGTTGGCTTGTTATAAATTAGCATAATACATGTCCATTTTTATCTTTTCCTTGTGTTGT AAACTTGCGTACACTATTTTACTATGTTGAGGTAAGGTAAGTCATGAGTATATTCATGAATAAC TCAAAATCTAATCTAGAGTTTTTCTTTTTAACTCCACCACTGGAATATAGTACCCTCTACCCGC TAGCCTCTATATCAACCCCAATCTGCTATGACCCTGCTATATGCTATTTAGAACTTTGCTTGCC ATTGCTAAACAAATGCTCTCAGTCATAAACAAATGATCTTTCTTCTCCAACATGGTATAAATGA ATGGCCAAAATTTCATTTAATCTACCCTTTTTATCCTTATGAATAAGTCTACAATGAGAACGGA GTAGCTATCCATAATCTATTTGTTCTCGATTGATCAAAGAGTATGTTGATGTACTATCAGTTAA ATAATTGCACAACCTCAACTGATCGAAGAAATGGCAAAGGTGCTCGCAAGCCATGAATGCTTGT TACTCGGAGAGTCCATCTCACGCATTTTTCTGCAAAACAAAAGCAGTGGTGCGGTTTGAGTTAA TAAGCAATTCAAATCTATCTTCTAGGATAAAACAGGCTAAAATATCATTTTGTCCATCGAGTTG TTGAGATGATACCGAGAATTGCTAAGGAAGATCCTATGAAAAAATACTATTATTTATGGATGGA CACAACATAAAATAACCGTGTATCACATTTGGTAGTATGCCTATGATATTGAGACTATAGTTCG AAATAACCTGATAATTCTTGTTGTTCAACATCTAACTAATGATACAGCTTTAATGATAACAGTA TTCAGCTTTATTAACTAACCTCAGTTTGTTGTACGTAACTAAAAGCAATGTTCAAAACTAGATA AGAATGACAATGCGAGAGATGGTGAGATGATCGTACTTTTGACCGAGTTCCGGAGACTAATTTG AACAAAGTCAGTACGAATATATGGAGGGATACGCAGATTCATCATATACATAACCCCAGCAATG ACCTGCACTAACACGGTTAAATAGCTACCGCAAGGGGATGAAATAGAAACAAATGAAACTCACT AACATACCTACCTTATCCACAAGTCCATGAATGACAAGGCTTGCCTTTTTATCCTTCGGAGTTG CCTGAATACGAAGGAGACAAGAAATGAAAAAAAAATATCTGTCTGCATCTCTTTTGGGGATTTA TCACATGTCATTGTAAACTTTCAATATTTATCTACATTACAAATATACATATATCCATATATGA CAATGTAATCTATGTTTATTAATTATTATATTACAATCTTGACCATTAAAAGGCTCATTTTTTT AAGATGAGCAAAATGACCAATGTTGTATTTTGAAAATTCTGGAAGTATAACCACTTAGTAGATT TCACATTTTAAAAACTACTCCCTCCAATCCTTAATAGATGATGTATTAGAATTTTGCTCATCAG CCAAGACACCTGTGTAAAAGACCAAATTGTCTTCATTGTTATGAGCATCATAGGGTTAGGGTCT GAAGACCGAGATTAGAATTAGGGCTCTGGCCCTTGGTCAACCATTCAGCCAGCCAGGAGCTCTT CCAAACCACTAGTCACCAGCTAAAGGCACTAGACTGTATTGGAGAATAGAGGAAAACTAGAATC CATCATTCCTTGTTACCCAAAAGTGTGTCACAATAACCTTCTGTCCTAGGCATCTCCAAATCAA AGAAGAATGGTAACAACTTGTGCAAGTGCAACTAATAACTAACCAAAATATATAATAAAGCAAT AACTGGTCTCTAAATTCTAACTTACTCGCCCTCTCTCCTGCCTTTAACTGGCATAACACCTCTG CTGGTTACTGTGTGATAACTCCTACTGCACCATGTCTCATATAGCTCCGTCTAATATGGCTCCA TGCAGCCATGGCAAAACATCATTTAATTCATTCATTAGCTGTCACGGGCATTAGGTCATGAGGC CAAGGCCCATGGATAGCCCATACCAGTTAAGTTAGAGATAAGATAAGATTGAATCTTACTTAGG GGTCAAGTTGTACCATCTATAAAAGGATGGGATTATGTCTATTATCAATTAAGCAATGAATATC AATTAGTCTAATATCTCCCTTCCCGTAATGTTCTTCTCCCTAGCCTAAATCTACATCCCTTCTC CACGAGCCGACGCCACCCAGTTATCCTCCCGGCGGTGGTTATCTCGCCATGGCCTTGGGTTGTG ACATTAGCTCAGTCATATGCCTATTTGAAATGAACAGTTGGCTGCACATTCAAAACTAGCACAT GAATGAACCCATGAGCATGTGTAATCGAATATTTGAGAAATATGGATGGAAAGCATGTATTTAT GGTTCTTTGGATTGTACATAACCTGATTAAGTCTATACTAGTAAATGCCCTTTGGATGGTTATG CTTGGGAAGGTAAAATTCAAATAACATTGCATTATGAAGGAAGGGGTATATAGGACAGACAAGT AAAAAGTTGTCTTGAGGTGATAGTATGATTTATATCTGGGAACAAAATATTAACCTAGAATGCA AATATTCAAAAATGGAGAGAGCAAAAGTTGCATCAATTGTACACCATGTGCATGTAAATACCAT ATTTGCAATTTCTAACTTTATAATGGATCAGGAATCCAATTATAAACCCCAAGTCTAAGTATAC AAGTTGAAGCAGTACAAACTACAAATTTTGTCAGAAGCATAAAGAAACAGCCATATAACAAACT TGAAATTTCCAAAACATGCCAAAAGATATTTTAATAATTTATATGTAGCCATAAATACTAACAT CCATGAGTTGAGTCATAGTTTAGTGCTACATAGAAAGACCTTACGAAGGAAGAACCATAACGTG CATTCAATTTAGTGCTTCTCAAGACTTAATATTGTTATTTAGTTGCACGTACCTGAAGATTTAC AATAGCCACCCTCCCCCCATTCTTCAGTGACAACAGAGGCATATTACAAGCAGGAGTAATCTGC AGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.094134685

Conservation Information
Conserved circRNAs	NA
PMCS	0.094134685

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11317857-11319735(-)
11319778-11321755(-)
						
						Potential amino acid sequence
						
							MVAAVRALPLNGLLIFCLQITPACNMPLLSLKNGGRVAIVNLQATPKDKKASLVIHGLVDKVGH
CWGYVYDESAYPSIYSY*(-)
MYMMNLRIPPYIRTDFVQISLRNSVKKKCVRWTLRVTSIHGLRAPLPFLRSVEVSFPERPDMKP
VVLKEQPFSLQRETSMNRPFVMLLTFNFSDGCGCSSSSIEWPVDFLSADYSCL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11317857-11319735(-) 11319778-11321755(-)
Potential amino acid sequence	MVAAVRALPLNGLLIFCLQITPACNMPLLSLKNGGRVAIVNLQATPKDKKASLVIHGLVDKVGH CWGYVYDESAYPSIYSY(-) MYMMNLRIPPYIRTDFVQISLRNSVKKKCVRWTLRVTSIHGLRAPLPFLRSVEVSFPERPDMKP VVLKEQPFSLQRETSMNRPFVMLLTFNFSDGCGCSSSSIEWPVDFLSADYSCL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0271000_circ_g.1

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